Carpenter, who grew up in Boulder and lived in Vail, Colo., died Oct. 10 of complications from a stroke in September. He was 88.
He was the second American to orbit the Earth, following John Glenn. Glenn is scheduled to speak at Carpenter's funeral.
Carpenter's family held a private service Saturday followed immediately by the public service. Six Navy officers carried Carpenter's flag-draped casket from a hearse into the church.
His ashes will be interred at his ranch near Steamboat Springs, Colo.
Glenn and Carpenter were the last survivors of NASA's famed Mercury program, which sent astronauts into space in one-person capsules. When Glenn blasted off, Carpenter was heard on the television broadcast saying, "Godspeed, John Glenn."
Carpenter orbited Earth three times in May 1962. After an instrument malfunctioned and he ran low on fuel, Carpenter had to take manual control and missed his landing target by 288 miles, but was found safe.
"I had made mistakes and some things had gone wrong," Carpenter recalled in the 1962 book "We Seven," written by the first seven astronauts. "But I hoped that other men could learn from my experiences. I felt that the flight was a success, and I was proud of that."
The troubled flight created a rift between Carpenter and NASA bosses, so he turned to sea exploration. In 1965, he spent 30 days under the ocean off the California coast in the Navy's SeaLab II program.
He returned to NASA in the 1960s to help develop the Apollo lunar lander. He then went back to the SeaLab program as director of aquanaut operations for SeaLab III.
He retired from the Navy in 1969 and founded his company Sea Sciences Inc.
He is survived by his wife, Patty Carpenter, and six children. Two other children died before him.